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Vital Signs with Dr. Sanjay Gupta

Analysts Examine the Human Microbiome's Impact on Health and Disease. Aired 2:30-3p ET

Aired September 16, 2017 - 14:30   ET



[14:30:27] DR. SANJAY GUPTA, CNN CHIEF MEDICAL CORRESPONDENT: You've probably heard that expression you are what you eat. Well, there's a lot more truth to that than you might think. It all comes down to a few bacteria, 100 trillion of them to be exact. That makes up what is known as the microbiome.

This is "Vital Signs." I'm Dr. Sanjay Gupta.

Microbes live in us and on us. In fact we have more bacteria than cells in our bodies, as many as 10 times more. These bacteria, specifically the ones in the stomach and intestines, impact nearly every aspect of our health from sleep to disease to diet, and it's influenced not only by what we put into our bodies but also by what's around us.

This diagram may look like a constellation chart. It's actually a map of bacteria taken from people all over the globe, and you probably have some of these living in you right now.

ROB KNIGHT, DIRECTOR, CENTER OF MICROBIOME INNOVATION, U.C. SAN DIEGO: There's more bacteria in your gut than there are stars in the universe by a long shot.

GUPTA: Rob Knight is mapping the human microbiome.

KNIGHT: The little dots are different kinds of bacteria. And we draw a line between two dots if that particular bacteria was found on that particular sample. And when we zoom out we see some very clear patterns.

GUPTA: What you see here is his brainchild, the American Gut Project. It's a citizen science research compilation, meaning the data is donated by the general public. It's also entirely crowd funded. For $99 U.S. dollars you can send your samples to the Knight Lab at U.C. San Diego and see what makes up your microbiome.

KNIGHT: By placing yourself on the map you'll be able to diagnose particular conditions, and what we hope ultimately be able to develop a kind of microbial GPS that helps you drive your microbiome around on this map defining where you are at the moment, where you would like to go in order to optimize your health.

GUPTA: This is the picture four years in with over 10,000 samples collected from 43 countries and counting. And they're only scratching the surface. So what do we know about these microbes?

KNIGHT: We know a tremendous about the microbiome compared to what we knew only a decade ago. Now for human stool sample, usually 97 percent to 99 percent of the sequences are identifiable. On the other hand we know very little about the functions, so it's like we have nametags for a lot of people at a party but we don't know what they do.

GUPTA: What makes this particularly hard is the diversity of microbiomes and that they change every day.

KNIGHT: Each of us is changing our microbiomes right now through things like the foods we eat, the spaces we live and work in, the people who we live and work with. But we're all 99.99 percent identical in terms of human genome, whereas you might be 90 percent different from the person you're sitting next to you in terms of your microbiome.

GUPTA: No two microbiomes are the same. It's unique to each of us. the microbiome is made of all the microbes in and on our body -- fungi, bacteria, viruses, for example. Most of these live if our gut, primarily in the large intestine. Researchers estimate that the total surface area of our gut is 3,000 square feet. That's larger than a tennis court. All those microbes outnumber our human cells about 10 to one, making us more bacteria than human. In fact if you weighed the microbiome it would be pounds. Think of how many microscopic bacteria and fungi it would take to add up to that weight. It's roughly 100 trillion of them in case you were wondering.

And while some might get grossed out with words like bacteria and fungi, the microbiome is the peacekeeper of our bodies, helping us digest our foods, fight disease, and regulate our immune system. Knight says that out of all these factors your diet has the biggest impact on your microbiome.

KNIGHT: It really matters a lot what you eat over the last six months to a year. One exception to that, though, is the number of different kinds of plants people eat. And that seems to have a very big impact on the microbiome. That sort of points to the observational nature of these studies like American Gut. You really need to take it into more well defined experiments to find out the connections and whether the microbiome is driving the difference in health or the difference in lifestyle, or whether the lifestyle is driving the microbiome.

GUPTA: This project could be game changing and potentially gut changing as well.

DR. EMBRIETTE HYDE, AMERICAN GUT PROJECT, U.C. SAN DIEGO: These microbes are involved in a number of diseases as varied as diabetes, autism, Parkinson's.

[14:35:03] And so this is another avenue or another piece to the puzzle. And so I really think that as we unravel the mysteries and figure out exactly how the microbiome is associated with these different diseases we'll be able to use that information to maybe improve diagnoses but also treatments as well. Meet Embriette Hyde, self-proclaimed microbial enthusiast and three

time tester of her own microbiome. She also manages the American Gut Project at U.C. San Diego.

HYDE: So when I took this sample, it was actually just after Thanksgiving in 2015 and I travelled to Michigan to visit my family. Diet certainly changed, but on top of that you can imagine that the weather in Michigan in November is a lot different from the weather in San Diego and Michigan. And so there's a lot of different components affecting my microbiome.

This was collected in January, 2016 after the holidays. I was pretty much just in my normal daily routine schedule. If you look at the list of the bacteria that were present in my sample, the top four of still the top four. And so that started to indicate to me that my microbiome was pretty stable over time.

So this third sample was taken about eight months after the second one, and this one is particularly interesting because this was collected on day seven of an antibiotic regimen. So I had probably lost half of the bacteria present in my sample after this antibiotic regimen. But what I found even more impressive about this was that my top four were still my top four, pretty stable across time at least over this year time period even though I'm doing different things daily to my microbiome that can have a big effect.

Being human isn't necessarily what we thought it was. We are a super- organism. We have our own cells but also these invisible microbial creatures living in us and on us. And they have a bigger effect on us than we really thought about before.


[14:40:30] GUPTA: Deep inside Venezuela's Amazon exists a bacteria gold mine, the good kind, belonging to a remote indigenous, seminomadic community. Undiscovered until 2008, the Yanomami happened to host the most diverse human microbiome every recorded.

MARIA GLORIA DOMINGUEZ-BELLO, MICROBIAL ANTHROPOLOGIST: They have about twice the diversity westernized U.S. population has.

GUPTA: Pristine microbiomes largely untouched by modern day medicine or members outside their community. Researchers wondered what have we lost and how?

DOMINGUEZ-BELLO: So these are extremely healthy people. And we want to understand what they have, how they function with their microbes. There is a lot of variation here.

GUPTA: Microbial anthropologist Maria Gloria Dominguez-Bello who piloted this research tested fecal, oral, and skin samples from 34 members of the Yanomami community. Her team found that the hunter gathers harbored anti-biotic resistant genes, suggesting it could be a natural feature of the human microbiome in an unaltered state.

DOMINGUEZ-BELLO: So want to understand what is it that is modulated by diet or may have disappeared with antibiotics that may not have been acquired from birth.

GUPTA: The first microbes a newborn receives comes from the mother's fluids if delivered vaginally, whereas infants born via Caesarian section do not. Some scientists theorize that these children may then miss out on important microbes that shape their immune system and their lifelong health.

DOMINGUEZ-BELLO: But every time we take an anti-biotic, and especially during very early age, the assembly of these communities is disrupted by the antibiotic. It's a tremendous effect because, by definition, antibiotics kill bacteria.

GUPTA: It is thought that antibiotics, rigorous hygiene practices, and highly processed foods, have decreased the diversity of microbiomes in the developed world.

DOMINGUEZ-BELLO: C-section and antibiotics we think are probably the major drivers, but also water. We drink chlorinated water. What is the effect of chlorinated water? We don't know that.

GUPTA: Scientists are hopeful that the key to driving optimal health lies within the microbiome.

DOMINGUEZ-BELLO: I think we have lost important microbes. I think -- our hypothesis is that we can restore them early in life, and then once the immune system is educated and the metabolic system, the crucial stage of the development is normalized, then those kids should have less allergies, asthma, celiac disease, type one diabetes, obesity. Eventually the whole world will converge into a single lifestyle.

I think the window is closing. More and more we go back to places and in a year we see that people have already been pretty much integrated. Of course, there is a big dilemma for them. They mostly want to remain in their lands, but they want technology and medicine. So is that achievable? I think so. But it's a big challenge.

GUPTA: A snapshot of a culture suspected to have been left alone for some 11,000 years. These Amazonian samples can perhaps give us some insight into how our microbiomes have evolved and possibly help treat chronic illnesses.

GUPTA: The microbiome is such a fascinating window into our health and our environment. In fact one laboratory in Boston has discovered that it can save lives as well. As my colleague, senior medical correspondent Elizabeth Cohen explains, one man's waste is another man's medicine.


UNIDENTIFIED MALE: Today is the big day.

ELIZABETH COHEN, CNN SENIOR MEDICAL CORRESPONDENT: For Eric, a 24- year-old research assistant at MIT, nature is calling, so he hops a train and then a bus. He passes countless toilets but doesn't use them, only stopping a full 30 minutes later inside this men's room. UNIDENTIFIED MALE: I'm going to put this down first, and then this,

and then I'm going to close the lid.

COHEN: Eric is a poop donor, and a pit stop here can save lives.

Eric, how is it going in there?

UNIDENTIFIED MALE: Things are going smoothly.

[14:45:00] COHEN: Good, good. So is this just like regular popping or do you do something special?

UNIDENTIFIED MALE: It is as normal as can be.

COHEN: This is OpenBiome. They've developed a way to turn poop into a treatment for Clostridium difficile. The infection kills 15,000 Americans a year and sickens half a million.

UNIDENTIFIED MALE: I have donated 29 times, which has resulted in 133 treatments, which is pretty great. And that has resulted in about $1,000.

COHEN: And 97 percent of people who want to donate poop are rejected, maybe because they've recently traveled to certain places or used antibiotics or gotten a tattoo.

UNIDENTIFIED FEMALE: This, I would say is a Bristol five.

COHEN: Lab technician Christina Kim demonstrates how they make the treatment. Poop that's too hard or too soft won't work.

It's very descriptive like a dry sausage, soft logs. Did you make this?

UNIDENTIFIED FEMALE: No. It's actually an established medical chart.

COHEN: A saline solution is added, then it gets sloshed around to filter out fiber. What's left behind is a liquid teaming with healthy bacteria.

This is either administered bottom up through a colonoscopy, or top down through a tube.

UNIDENTIFIED FEMALE: Yes, a tube that travels all the way from your nose down to your intestines, our target area of delivery.

COHEN: So the healthy microbes from Eric's poop will sort of chase out the sick microbes that the patient has.


COHEN: It's called a fecal transplant. Inside this freezer, the 133 treatments Eric's provided. The bacteria inside them are still alive, cryogenically preserved at negative 112 degrees.

UNIDENTIFIED MALE: I never thought I would be staring at my poop frozen in a freezer destined to help people across the country. That's really cool.

COHEN: Did you do all this for the money?

UNIDENTIFIED MALE: No. The money was nice for sure, but it's about helping people.



GUPTA: For Joe Cobucci, everything healthy day is a blessing. Joe has Crohn's, an autoimmune disease that causes inflammation of the digestive tract. Crohn's may slow Joe down from time to time, but he keeps on running, 58 half marathons and counting.

JOE COBUCCI: So here's a few of my medals over the many years, but there's some ones that really stick out that mean a lot to me. This specific one right here is my first marathon.

So I was diagnosed at age 11 with Crohn's disease. And that was a little over 40 years ago, so I've lived this struggle for a long time. The physician thought I had like a mental illness. He thought I had extreme anxiety because he didn't understand why I didn't want to leave the home.

GUPTA: Crohn's is a type of inflammatory bowel disease, Symptoms are debilitating, often embarrassing for sufferers. They include severe diarrhea, abdominal pain, and fatigue.

COBUCCI: I have to say I'm a GPS for restrooms. I always carry a change of clothes with me just in case no matter where I'm going.

GUPTA: But what really is Crohn's disease? And what does it have to do with the microbiome?


GUPTA: Dr. Doug Wolf has been diagnosing inflammatory bowel diseases for 25 years. And he says some case respond better to medicine, and some by tweaking the microbiome.

WOLF: The challenge that lies ahead, to really be better at understanding and sorting out Crohn's disease, ulcerative colitis, the IBD one through 10 or 20, then better direct personalize our care, target our treatments, and do a better job.

GUPTA: How would you describe how well we understand Crohn's disease, ulcerative colitis? Where are we in understanding these diseases?

WOLF: We're somewhere between the first inning and the ninth inning. Our understanding of genetics is great but very shallow. But it's not all genetics.

GUPTA: Currently, there is no cure for the chronic condition, and about 80 percent will eventually need surgery.

WOLF: The best thing is to get an early diagnosis, early management, control the inflammation and thereby really change the course of the disease.

COBUCCI: Over the years it's just been times when I've been very, very ill, and times I've been really healthy. But with Crohn's or ulcerative colitis it can change in a second. So it's challenging because you can go to the restroom, it's hard to say, but 20 to 30 times a day. Think about that, 20 to 30 times a day to use the restroom. The digestive issues and the pain for that is challenging. It really is. It is just -- aches and pains all around. This disease dictates my life. I've built my life around it, which is one reason why working for the foundation is so important for me.

GUPTA: Joe is a national team manager for Team Challenge, the Crohn's and Colitis Foundation's endurance training and fundraising program.

COBUCCI: I found the foundation in a very odd way. I was getting a colonoscopy and saw a flyer for the Crohn's and Colitis Foundation's team challenge half marathon program. So I called the number on the back of the flyer, and that changed my life forever. I went to a meeting which was the following morning. I went in there and was in a room with about 50 people, and I had never been around anybody who had Crohn's or colitis, and I got very emotional. I started to cry. And I fell in love with this program and found a new family.

GUPTA: The exact cause of Crohn's remain as mystery. Some have argued that bad microbes may prompt it, or that a missing microbe is the cause for the inflammation.

Could you predict if someone is more likely to develop inflammatory bowel disease based on their microbiome?

WOLF: We're really at the tip of the iceberg, but I think that it's pretty clear that there is importance to the microbiome and there are things that we can do to tweak it.

GUPTA: What do the treatment options look like now for someone who has Crohn's disease?

[14:55:00] WOLF: So now we've got at least seven biologics for Crohn's disease and ulcerative colitis, and now we have to figure out how to use them best. Should it be for an indefinite period, or for a few years? We're not sure.

GUPTA: When you meet a patient and they now have this diagnosis of inflammatory bowel disease, you're having a first conversation with them, and they want to know what's my life going to be like, what do you tell them?

WOLF: There truly are no limits because of the diagnosis. People typically have normal lives and normal life expectancies.

GUPTA: Joe is the perfect example. COBUCCI: I love, love running. I can't begin to describe it to you.

Many, many races, it's hard to believe 58 of them have happened. Crohn's impacts me when I'm training or running. I'm always fearful of having to use the bathroom. I'm getting much better. I do procedure nutrition and I eat certain things I know that work for me. But it is something that I constantly think about.

GUPTA: Because the microbiome is constantly changing and differs from person to person, it's not yet clear how best to encourage and maintain a healthy gut. Research has potentially linked poor gut microbiomes with diseases as varied as Parkinson's, autism, obesity, and as we just saw, Crohn's and ulcerative colitis. And the key to treating illnesses and leading a healthy lifestyle may lie within the symbiotic relationship between microbes and humans.